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      Discovery and Genomic Characterization of a Novel Ovine Partetravirus and a New Genotype of Bovine Partetravirus

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          Abstract

          Partetravirus is a recently described group of animal parvoviruses which include the human partetravirus, bovine partetravirus and porcine partetravirus (previously known as human parvovirus 4, bovine hokovirus and porcine hokovirus respectively). In this report, we describe the discovery and genomic characterization of partetraviruses in bovine and ovine samples from China. These partetraviruses were detected by PCR in 1.8% of bovine liver samples, 66.7% of ovine liver samples and 71.4% of ovine spleen samples. One of the bovine partetraviruses detected in the present samples is phylogenetically distinct from previously reported bovine partetraviruses and likely represents a novel genotype. The ovine partetravirus is a novel partetravirus and phylogenetically most related to the bovine partetraviruses. The genome organization is conserved amongst these viruses, including the presence of a putative transmembrane protein encoded by an overlapping reading frame in ORF2. Results from the present study provide further support to the classification of partetraviruses as a separate genus in Parvovirinae.

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          Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.

          K Lole, R Bollinger, R S Paranjape … (1999)
          The development of an effective human immunodeficiency virus type 1 (HIV-1) vaccine is likely to depend on knowledge of circulating variants of genes other than the commonly sequenced gag and env genes. In addition, full-genome data are particularly limited for HIV-1 subtype C, currently the most commonly transmitted subtype in India and worldwide. Likewise, little is known about sequence variation of HIV-1 in India, the country facing the largest burden of HIV worldwide. Therefore, the objective of this study was to clone and characterize the complete genome of HIV-1 from seroconverters infected with subtype C variants in India. Cocultured HIV-1 isolates were obtained from six seroincident individuals from Pune, India, and virtually full-length HIV-1 genomes were amplified, cloned, and sequenced from each. Sequence analysis revealed that five of the six genomes were of subtype C, while one was a mosaic of subtypes A and C, with multiple breakpoints in env, nef, and the 3' long terminal repeat as determined by both maximal chi2 analysis and phylogenetic bootstrapping. Sequences were compared for preservation of known cytotoxic T lymphocyte (CTL) epitopes. Compared with those of the HIV-1LAI sequence, 38% of well-defined CTL epitopes were identical. The proportion of nonconservative substitutions for Env, at 61%, was higher (P < 0.001) than those for Gag (24%), Pol (18%), and Nef (32%). Therefore, characterized CTL epitopes demonstrated substantial differences from subtype B laboratory strains, which were most pronounced in Env. Because these clones were obtained from Indian seroconverters, they are likely to facilitate vaccine-related efforts in India by providing potential antigens for vaccine candidates as well as for assays of vaccine responsiveness.
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            Cloning of a human parvovirus by molecular screening of respiratory tract samples.

            Tobias Allander, Martti T Tammi, Margareta Eriksson … (2005)
            The identification of new virus species is a key issue for the study of infectious disease but is technically very difficult. We developed a system for large-scale molecular virus screening of clinical samples based on host DNA depletion, random PCR amplification, large-scale sequencing, and bioinformatics. The technology was applied to pooled human respiratory tract samples. The first experiments detected seven human virus species without the use of any specific reagent. Among the detected viruses were one coronavirus and one parvovirus, both of which were at that time uncharacterized. The parvovirus, provisionally named human bocavirus, was in a retrospective clinical study detected in 17 additional patients and associated with lower respiratory tract infections in children. The molecular virus screening procedure provides a general culture-independent solution to the problem of detecting unknown virus species in single or pooled samples. We suggest that a systematic exploration of the viruses that infect humans, "the human virome," can be initiated.
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              Evidence of human coronavirus HKU1 and human bocavirus in Australian children

              Theo Sloots, Peter McErlean, David J Speicher … (2005)
              Undiagnosed cases of respiratory tract disease suspected of an infectious aetiology peak during the winter months. Since studies applying molecular diagnostic assays usually report reductions in the number of undiagnosed cases of infectious disease compared to traditional techniques, we applied PCR assays to investigate the role of two recently described viruses, namely human coronavirus (HCoV) HKU1 and human bocavirus (HBoV), in a hospital-based paediatric population. Both viruses were found among Australia children with upper or lower respiratory tract disease during the autumn and winter of 2004, contributing to 21.1% of all microbial diagnoses, with individual incidences of 3.1% (HCoV-HKU1) and 5.6% (HBoV) among 324 specimens. HBoV was found to coincide with another virus in more than half of all instances and displayed a single genetic lineage, whilst HCoV-HKU1 was more likely to occur in the absence of another microbe and strains could be divided into two genetic lineages which we propose be termed HCoV-HKU1 type A and type B. Children under the age of 2 years were most at risk of infection by these viruses which contribute significantly to the microbial burden among patients with respiratory tract disease during the colder months.
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                Author and article information

                Contributors
                : Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2011
                Publication date (Electronic): 27 September 2011
                Volume: 6
                Issue: 9
                Electronic Location Identifier: e25619
                Affiliations
                [1 ]Department of Microbiology, The University of Hong Kong, Hong Kong, China
                [2 ]Research Centre of Infection and Immunity, The University of Hong Kong, Hong Kong, China
                [3 ]State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
                [4 ]Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
                [5 ]Shenzhen-Hong Kong Institute of Infectious Diseases, Shenzhen Institute of Hepatology, Shenzhen Third People's Hospital, Shenzhen, China
                [6 ]State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
                University of Kansas Medical Center, United States of America
                Author notes

                Conceived and designed the experiments: HT PCYW SKPL KYY. Performed the experiments: HWT JLLT. Analyzed the data: HT HWT JLLT. Contributed reagents/materials/analysis tools: XCC HL BZ BJZ PCYW SKPL KYY. Wrote the paper: HT KYY.

                Article
                Publisher ID: PONE-D-11-06317
                DOI: 10.1371/journal.pone.0025619
                PMC ID: 3181347
                PubMed ID: 21980506
                SO-VID: b7888c1e-1abf-41ff-83be-d92068ccc3c8
                Copyright statement: Tse et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                Date received : 1 April 2011
                Date accepted : 8 September 2011
                Page count
                Pages: 8
                Categories
                Subject: Research Article
                Subject: Biology
                Subject: Microbiology
                Subject: Virology
                Subject: Viral Classification
                Subject: DNA viruses
                Subject: Emerging Viral Diseases
                Subject: Viral Evolution
                Subject: Veterinary Science
                Subject: Veterinary Diseases
                Subject: Veterinary Virology

                ScienceOpen disciplines: Uncategorized
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                ScienceOpen disciplines: Uncategorized

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